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    SYNC syncoilin, intermediate filament protein [ Homo sapiens (human) ]

    Gene ID: 81493, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SYNCprovided by HGNC
    Official Full Name
    syncoilin, intermediate filament proteinprovided by HGNC
    Primary source
    HGNC:HGNC:28897
    See related
    Ensembl:ENSG00000162520 MIM:611750; AllianceGenome:HGNC:28897
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    SYNC1; SYNCOILIN
    Summary
    This gene encodes a member of the intermediate filament family which contains an N-terminal head domain, followed by a central coiled-coil region and a short C-terminal tail. The protein is highly expressed in skeletal and cardiac muscle. The protein links the dystrophin associated protein complex (DAPC) to desmin filaments in muscle and may have a structural role in striated muscle. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2009]
    Expression
    Ubiquitous expression in testis (RPKM 20.2), appendix (RPKM 15.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SYNC in Genome Data Viewer
    Location:
    1p35.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (32679906..32703593, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (32539693..32563413, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (33145507..33168371, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723870 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:33077607-33078108 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 694 Neighboring gene zinc finger and BTB domain containing 8 opposite strand Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33107487-33108246 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33108247-33109005 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 603 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 695 Neighboring gene hESC enhancers GRCh37_chr1:33116021-33116608 and GRCh37_chr1:33116609-33117197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 696 Neighboring gene RB binding protein 4, chromatin remodeling factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:33154443-33154943 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33160284-33161022 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33167839-33168604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33168605-33169370 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 607 Neighboring gene Sharpr-MPRA regulatory region 2185 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33183271-33184026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33189892-33190720 Neighboring gene Sharpr-MPRA regulatory region 8469 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33200787-33201312 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33201837-33202361 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33202362-33202885 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 608 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:33219766-33220279 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33225004-33225886 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33225887-33226770 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:33227405-33227625 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33231243-33232135 Neighboring gene NHS like 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33232136-33233029 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33235076-33235991 Neighboring gene Sharpr-MPRA regulatory region 15696 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_6796 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:33251929-33253128 Neighboring gene tyrosyl-tRNA synthetase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 697 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33269619-33270293 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33270294-33270967 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33275934-33276570 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33276571-33277206 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33282071-33282572 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:33282573-33283072 Neighboring gene S100P binding protein

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Elevated SYNC Expression Is Associated with Gastric Tumorigenesis and Infiltration of M2-Polarized Macrophages in the Gastric Tumor Immune Microenvironment. Wang D, et al. Genet Test Mol Biomarkers, 2021 Mar. PMID 33734892
    2. Syncoilin upregulation in muscle of patients with neuromuscular disease. Brown SC, et al. Muscle Nerve, 2005 Dec. PMID 16124004
    3. Syncoilin modulates peripherin filament networks and is necessary for large-calibre motor neurons. Clarke WT, et al. J Cell Sci, 2010 Aug 1. PMID 20587592, Free PMC Article
    4. Dysbindin, syncoilin, and beta-synemin mRNA levels in dystrophic muscles. Wakayama Y, et al. Int J Neurosci, 2010 Feb. PMID 20199207
    5. Syncoilin, a novel member of the intermediate filament superfamily that interacts with alpha-dystrobrevin in skeletal muscle. Newey SE, et al. J Biol Chem, 2001 Mar 2. PMID 11053421

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Elevated SYNC Expression Is Associated with Gastric Tumorigenesis and Infiltration of M2-Polarized Macrophages in the Gastric Tumor Immune Microenvironment.
      Title: Elevated SYNC Expression Is Associated with Gastric Tumorigenesis and Infiltration of M2-Polarized Macrophages in the Gastric Tumor Immune Microenvironment.
    2. Syncoilin modulates peripherin filament network formation.
      Title: Syncoilin modulates peripherin filament networks and is necessary for large-calibre motor neurons.
    3. The differences in human syncoilin and beta-synemin mRNA ratios between Duchenne muscular dystrophy and normal muscles were not statistically significant
      Title: Dysbindin, syncoilin, and beta-synemin mRNA levels in dystrophic muscles.
    4. the result of this study raise the possibility that mutations in the gene encoding for syncoilin may underlie some forms of muscle disease.
      Title: Syncoilin upregulation in muscle of patients with neuromuscular disease.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC149625, MGC149626

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in intermediate filament-based process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in Z disc IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in intermediate filament IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in neuromuscular junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in perinuclear region of cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in sarcolemma IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    syncoilin
    Names
    intermediate filament protein syncoilin
    syncoilin intermediate filament 1
    syncoilin-1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_012421.2 RefSeqGene

      Range
      5823..28687
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001161708.2 → NP_001155180.2  syncoilin isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon, compared to variant 1, that causes a frameshift. The resulting protein (isoform 2) has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC114489
      Consensus CDS
      CCDS53294.1
      Related
      ENSP00000362583.3, ENST00000373484.4
      Conserved Domains (1) summary
      pfam00038
      Location:170 → 457
      Filament; Intermediate filament protein

    2. NM_030786.3 → NP_110413.3  syncoilin isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC114489
      Consensus CDS
      CCDS367.2
      UniProtKB/Swiss-Prot
      B4DNK8, B4DY58, C9IY41, Q9H7C4
      Related
      ENSP00000386439.3, ENST00000409190.8
      Conserved Domains (1) summary
      pfam00038
      Location:170 → 456
      Filament; Intermediate filament protein

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      32679906..32703593 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047431210.1 → XP_047287166.1  syncoilin isoform X3

    2. XM_047431230.1 → XP_047287186.1  syncoilin isoform X3

    3. XM_047431221.1 → XP_047287177.1  syncoilin isoform X3

    4. XM_024450013.2 → XP_024305781.1  syncoilin isoform X2

      Conserved Domains (1) summary
      pfam00038
      Location:82 → 368
      Filament; Intermediate filament protein

    5. XM_024450010.2 → XP_024305778.1  syncoilin isoform X1

      Conserved Domains (1) summary
      pfam00038
      Location:170 → 456
      Filament; Intermediate filament protein

    6. XM_024450011.2 → XP_024305779.1  syncoilin isoform X2

      Conserved Domains (1) summary
      pfam00038
      Location:82 → 368
      Filament; Intermediate filament protein

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      32539693..32563413 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338892.1 → XP_054194867.1  syncoilin isoform X3

    2. XM_054338894.1 → XP_054194869.1  syncoilin isoform X3

    3. XM_054338893.1 → XP_054194868.1  syncoilin isoform X3

    4. XM_054338890.1 → XP_054194865.1  syncoilin isoform X2

    5. XM_054338889.1 → XP_054194864.1  syncoilin isoform X1

    6. XM_054338891.1 → XP_054194866.1  syncoilin isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H7C4.3 GenPept UniProtKB/Swiss-Prot:Q9H7C4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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